The object of this research aims at the hydraulic generator unit rotor system. According to fault problems of the generator rotor local rubbing caused by the parallel misalignment and mass eccentricity, a dynamic model for the rotor system coupled with misalignment and rub-impact is established. The dynamic behaviors of this system are investigated using numerical integral method, as the parallel misalignment, mass eccentricity and bearing stiffness vary. The nonlinear dynamic responses of the generator rotor and turbine rotor with coupling faults are analyzed by means of bifurcation diagrams, Poincaré maps, axis orbits, time histories and amplitude spectrum diagrams. Various nonlinear phenomena in the system, such as periodic, three-periodic and quasi-periodic motions, are studied with the change of the parallel misalignment. The results reveal that vibration characteristics of the rotor system with coupling faults are extremely complex and there are some low frequencies with large amplitude in the 0.3-0.4× components. As the increase in mass eccentricity, the interval of nonperiodic motions will be continuously moved forward. It suggests that the reduction in mass eccentricity or increase in bearing stiffness could preclude nonlinear vibration. These might provide some important theory references for safety operating and exact identification of the faults in rotating machinery.